7DHW
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7dhw by Molmil](/molmil-images/mine/7dhw) | Crystal structure of myosin-XI motor domain in complex with ADP-ALF4 | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, MAGNESIUM ION, ... | Authors: | Suzuki, K, Haraguchi, T, Tamanaha, M, Yoshimura, K, Imi, T, Tominaga, M, Sakayama, H, Nishiyama, T, Ito, K, Murata, T. | Deposit date: | 2020-11-17 | Release date: | 2021-05-19 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.84 Å) | Cite: | Discovery of ultrafast myosin, its amino acid sequence, and structural features. Proc.Natl.Acad.Sci.USA, 119, 2022
|
|
1X3U
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1x3u by Molmil](/molmil-images/mine/1x3u) | Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium melilot | Descriptor: | Transcriptional regulatory protein fixJ | Authors: | Kurashima-Ito, K, Kasai, Y, Hosono, K, Tamura, K, Oue, S, Isogai, M, Ito, Y, Nakamura, H, Shiro, Y. | Deposit date: | 2005-05-10 | Release date: | 2006-05-02 | Last modified: | 2024-05-29 | Method: | SOLUTION NMR | Cite: | Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium meliloti and its recognition of the fixK promoter Biochemistry, 44, 2005
|
|
5B3S
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 5b3s by Molmil](/molmil-images/mine/5b3s) | Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K) | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | Authors: | Shimada, A, Shinzawa-Ito, K, Yoshikawa, S, Tsukihara, T. | Deposit date: | 2016-03-11 | Release date: | 2017-03-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.68 Å) | Cite: | Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K) To Be Published
|
|
4U4V
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4u4v by Molmil](/molmil-images/mine/4u4v) | Structure of a nitrate/nitrite antiporter NarK in apo inward-open state | Descriptor: | NICKEL (II) ION, Nitrate/nitrite transporter NarK, OLEIC ACID | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | Deposit date: | 2014-07-24 | Release date: | 2015-07-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK Nat Commun, 6, 2015
|
|
4U4W
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4u4w by Molmil](/molmil-images/mine/4u4w) | Structure of a nitrate/nitrite antiporter NarK in nitrate-bound occluded state | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, NITRATE ION, Nitrate/nitrite transporter NarK, ... | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | Deposit date: | 2014-07-24 | Release date: | 2015-07-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK Nat Commun, 6, 2015
|
|
4U4T
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4u4t by Molmil](/molmil-images/mine/4u4t) | Structure of a nitrate/nitrite antiporter NarK in nitrate-bound inward-open state | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, NITRATE ION, Nitrate/nitrite transporter NarK, ... | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | Deposit date: | 2014-07-24 | Release date: | 2015-07-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK Nat Commun, 6, 2015
|
|
1ZOV
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1zov by Molmil](/molmil-images/mine/1zov) | Crystal Structure of Monomeric Sarcosine Oxidase from Bacillus sp. NS-129 | Descriptor: | CHLORIDE ION, FLAVIN-ADENINE DINUCLEOTIDE, Monomeric sarcosine oxidase | Authors: | Nagata, K, Sasaki, H, Ohtsuka, J, Hua, M, Okai, M, Kubota, K, Kamo, M, Ito, K, Ichikawa, T, Koyama, Y, Tanokura, M. | Deposit date: | 2005-05-14 | Release date: | 2006-05-23 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.86 Å) | Cite: | Crystal structure of monomeric sarcosine oxidase from Bacillus sp. NS-129 reveals multiple conformations at the active-site loop PROC.JPN.ACAD.,SER.B, 81, 2005
|
|
5AWH
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 5awh by Molmil](/molmil-images/mine/5awh) | Rhodobacter sphaeroides Argonaute in complex with guide RNA/target DNA heteroduplex | Descriptor: | DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3'), MAGNESIUM ION, RNA (5'-D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'), ... | Authors: | Miyoshi, T, Ito, K, Murakami, R, Uchiumi, T. | Deposit date: | 2015-07-03 | Release date: | 2016-07-06 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute. Nat Commun, 7, 2016
|
|
1WM1
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1wm1 by Molmil](/molmil-images/mine/1wm1) | Crystal Structure of Prolyl Aminopeptidase, Complex with Pro-TBODA | Descriptor: | (5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)[(2R)-PYRROLIDIN-2-YL]METHANONE, Proline iminopeptidase | Authors: | Nakajima, Y, Inoue, T, Ito, K, Tozaka, T, Hatakeyama, S, Tanaka, N, Nakamura, K.T, Yoshimoto, T. | Deposit date: | 2004-07-01 | Release date: | 2004-07-20 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Novel inhibitor for prolyl aminopeptidase from Serratia marcescens and studies on the mechanism of substrate recognition of the enzyme using the inhibitor ARCH.BIOCHEM.BIOPHYS., 416, 2003
|
|
2HI7
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2hi7 by Molmil](/molmil-images/mine/2hi7) | Crystal structure of DsbA-DsbB-ubiquinone complex | Descriptor: | Disulfide bond formation protein B, Thiol:disulfide interchange protein dsbA, UBIQUINONE-1, ... | Authors: | Inaba, K, Murakami, S, Suzuki, M, Nakagawa, A, Yamashita, E, Okada, K, Ito, K. | Deposit date: | 2006-06-29 | Release date: | 2006-12-05 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (3.7 Å) | Cite: | Crystal Structure of the DsbB-DsbA Complex Reveals a Mechanism of Disulfide Bond Generation Cell(Cambridge,Mass.), 127, 2006
|
|
1X2E
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1x2e by Molmil](/molmil-images/mine/1x2e) | The crystal structure of prolyl aminopeptidase complexed with Ala-TBODA | Descriptor: | (2S)-2-AMINO-1-(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)PROPAN-1-ONE, Proline iminopeptidase | Authors: | Nakajima, Y, Ito, K, Sakata, M, Xu, Y, Matsubara, F, Hatakeyama, S, Yoshimoto, T. | Deposit date: | 2005-04-22 | Release date: | 2006-05-09 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Unusual extra space at the active site and high activity for acetylated hydroxyproline of prolyl aminopeptidase from Serratia marcescens J.Bacteriol., 188, 2006
|
|
1X2B
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1x2b by Molmil](/molmil-images/mine/1x2b) | The crystal structure of prolyl aminopeptidase complexed with Sar-TBODA | Descriptor: | 1-(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)-2-(METHYLAMINO)ETHANONE, Proline iminopeptidase | Authors: | Nakajima, Y, Ito, K, Sakata, M, Xu, Y, Matsubara, F, Hatakeyama, S, Yoshimoto, T. | Deposit date: | 2005-04-22 | Release date: | 2006-05-09 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Unusual extra space at the active site and high activity for acetylated hydroxyproline of prolyl aminopeptidase from Serratia marcescens J.Bacteriol., 188, 2006
|
|
2IPC
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2ipc by Molmil](/molmil-images/mine/2ipc) | Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer | Descriptor: | Preprotein translocase SecA subunit | Authors: | Vassylyev, D.G, Mori, H, Vassylyeva, M.N, Tsukazaki, T, Kimura, Y, Tahirov, T.H, Ito, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2006-10-12 | Release date: | 2006-11-28 | Last modified: | 2024-02-21 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal Structure of the Translocation ATPase SecA from Thermus thermophilus Reveals a Parallel, Head-to-Head Dimer. J.Mol.Biol., 364, 2006
|
|
1V7Z
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1v7z by Molmil](/molmil-images/mine/1v7z) | creatininase-product complex | Descriptor: | MANGANESE (II) ION, N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE, SULFATE ION, ... | Authors: | Yoshimoto, T, Tanaka, N, Kanada, N, Inoue, T, Nakajima, Y, Haratake, M, Nakamura, K.T, Xu, Y, Ito, K. | Deposit date: | 2003-12-26 | Release date: | 2004-01-27 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism J.Mol.Biol., 337, 2004
|
|
1UGP
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1ugp by Molmil](/molmil-images/mine/1ugp) | Crystal structure of Co-type nitrile hydratase complexed with n-butyric acid | Descriptor: | COBALT (II) ION, Cobalt-containing nitrile hydratase subunit alpha, Cobalt-containing nitrile hydratase subunit beta, ... | Authors: | Miyanaga, A, Fushinobu, S, Ito, K, Shoun, H, Wakagi, T. | Deposit date: | 2003-06-17 | Release date: | 2004-06-17 | Last modified: | 2022-12-21 | Method: | X-RAY DIFFRACTION (1.63 Å) | Cite: | Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding Eur.J.Biochem., 271, 2004
|
|
1UGS
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1ugs by Molmil](/molmil-images/mine/1ugs) | Crystal structure of aY114T mutant of Co-type nitrile hydratase | Descriptor: | COBALT (II) ION, Nitrile Hydratase alpha subunit, Nitrile Hydratase beta subunit | Authors: | Miyanaga, A, Fushinobu, S, Ito, K, Shoun, H, Wakagi, T. | Deposit date: | 2003-06-17 | Release date: | 2004-06-17 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding Eur.J.Biochem., 271, 2004
|
|
1UGR
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1ugr by Molmil](/molmil-images/mine/1ugr) | Crystal structure of aT109S mutant of Co-type nitrile hydratase | Descriptor: | COBALT (II) ION, Nitrile Hydratase alpha subunit, Nitrile Hydratase beta subunit | Authors: | Miyanaga, A, Fushinobu, S, Ito, K, Shoun, H, Wakagi, T. | Deposit date: | 2003-06-17 | Release date: | 2004-06-17 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding Eur.J.Biochem., 271, 2004
|
|
1UGQ
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1ugq by Molmil](/molmil-images/mine/1ugq) | Crystal structure of apoenzyme of Co-type nitrile hydratase | Descriptor: | Nitrile Hydratase alpha subunit, Nitrile Hydratase beta subunit | Authors: | Miyanaga, A, Fushinobu, S, Ito, K, Shoun, H, Wakagi, T. | Deposit date: | 2003-06-17 | Release date: | 2004-06-17 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding Eur.J.Biochem., 271, 2004
|
|
1V3Y
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1v3y by Molmil](/molmil-images/mine/1v3y) | The crystal structure of peptide deformylase from Thermus thermophilus HB8 | Descriptor: | Peptide deformylase | Authors: | Kamo, M, Kudo, N, Lee, W.C, Ito, K, Motoshim, H, Tanokura, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-11-07 | Release date: | 2004-12-28 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.81 Å) | Cite: | The crystal structure of peptide deformylase from Thermus thermophilus HB8 to be published
|
|
5YT0
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 5yt0 by Molmil](/molmil-images/mine/5yt0) | Crystal structure of the complex of archaeal ribosomal stalk protein aP1 and archaeal translation initiation factor aIF5B | Descriptor: | Archaeal ribosomal stalk protein aP1, GUANOSINE-5'-DIPHOSPHATE, Probable translation initiation factor IF-2 | Authors: | Murakami, R, Singh, C.R, Morris, J, Tang, L, Harmon, I, Miyoshi, T, Ito, K, Asano, K, Uchiumi, T. | Deposit date: | 2017-11-16 | Release date: | 2018-06-27 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | The Interaction between the Ribosomal Stalk Proteins and Translation Initiation Factor 5B Promotes Translation Initiation Mol. Cell. Biol., 38, 2018
|
|
3J9W
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3j9w by Molmil](/molmil-images/mine/3j9w) | Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein bS16, ... | Authors: | Sohmen, D, Chiba, S, Shimokawa-Chiba, N, Innis, C.A, Berninghausen, O, Beckmann, R, Ito, K, Wilson, D.N. | Deposit date: | 2015-03-16 | Release date: | 2015-04-29 | Last modified: | 2024-02-21 | Method: | ELECTRON MICROSCOPY (3.9 Å) | Cite: | Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling. Nat Commun, 6, 2015
|
|
7CSL
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7csl by Molmil](/molmil-images/mine/7csl) | Crystal structure of the archaeal EF1A-EF1B complex | Descriptor: | Elongation factor 1-alpha, Elongation factor 1-beta | Authors: | Suzuki, T, Ito, K, Miyoshi, T, Murakami, R, Uchiumi, T. | Deposit date: | 2020-08-15 | Release date: | 2021-06-23 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural insights into the Switching Off of the Interaction between the Archaeal Ribosomal Stalk and aEF1A by Nucleotide Exchange Factor aEF1B. J.Mol.Biol., 433, 2021
|
|
5FG3
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 5fg3 by Molmil](/molmil-images/mine/5fg3) | Crystal structure of GDP-bound aIF5B from Aeropyrum pernix | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Probable translation initiation factor IF-2 | Authors: | Murakami, R, Miyoshi, T, Uchiumi, T, Ito, K. | Deposit date: | 2015-12-20 | Release date: | 2016-05-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystal structure of translation initiation factor 5B from the crenarchaeon Aeropyrum pernix. Proteins, 84, 2016
|
|
1BK1
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1bk1 by Molmil](/molmil-images/mine/1bk1) | ENDO-1,4-BETA-XYLANASE C | Descriptor: | ENDO-1,4-B-XYLANASE C | Authors: | Fushinobu, S, Ito, K, Konno, M, Wakagi, T, Matsuzawa, H. | Deposit date: | 1998-07-14 | Release date: | 1999-01-13 | Last modified: | 2023-08-02 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH. Protein Eng., 11, 1998
|
|
5YV5
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 5yv5 by Molmil](/molmil-images/mine/5yv5) | Crystal structure of the complex of archaeal ribosomal stalk protein aP1 and archaeal ribosome recycling factor aABCE1. | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ATPase RIL, Archaeal ribosomal stalk protein aP1, ... | Authors: | Imai, H, Abe, T, Miyoshi, T, Nishikawa, S, Ito, K, Uchiumi, T. | Deposit date: | 2017-11-24 | Release date: | 2018-07-18 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | The ribosomal stalk protein is crucial for the action of the conserved ATPase ABCE1 Nucleic Acids Res., 46, 2018
|
|